This series of files compile all analyses done during Chapter 2:

All analyses have been done with R 3.6.3.

Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it

Sources of activity considered for the analyses:

Fisheries data considered for the analyses (expressed as number of fishing events or kilograms of collected individuals for each gear):

Gear Code Years Events Species
Trap TrapFish 2010-2015 1061 Buccinum sp., Cancer irroratus, Chionoecetes opilio, Homarus americanus
Bottom-trawl TrawFish 2013-2014 2 Pandalus borealis
Net NetFish 2010 5 Clupea harengus, Gadus morhua
Dredge DredFish 2010-2014 21 Mactromeris polynyma

1. Explorations

1.1. Relationships between parameters

This section explores relationships between human activity exposure indices (dependant variables) and biotic and abiotic parameters (predictors).

Fist, we can compute the Spearman’s correlation coefficients.

Correlation coefficients between habitat parameters and metals concentrations
  om gravel sand silt clay arsenic cadmium chromium copper iron manganese mercury lead zinc S N H J aquaculture city dredging_collect dredging_dump industry shipping_mooring shipping_traffic sewers_rain sewers_waste wharves_city wharves_industry fisheries_trap fisheries_trawl fisheries_net fisheries_dredge cumulative_influence
om 1 -0.379 -0.708 0.68 0.023 0.57 0.486 0.606 0.593 0.586 0.568 0.537 0.587 0.605 -0.026 -0.121 0.122 0.136 -0.41 -0.033 0.22 0.43 0.309 0.518 0.291 0.239 0.401 -0.073 0.366 -0.508 -0.213 0.004 -0.238 0.274
gravel -0.379 1 0.186 -0.471 0.099 -0.127 -0.23 -0.194 -0.23 -0.232 -0.199 -0.207 -0.169 -0.235 0.029 0.007 0.012 0.07 0.143 -0.068 -0.175 -0.161 -0.081 -0.216 -0.02 0 -0.073 -0.061 -0.166 0.16 0.172 -0.055 0.068 -0.12
sand -0.708 0.186 1 -0.788 -0.308 -0.648 -0.504 -0.587 -0.483 -0.407 -0.524 -0.611 -0.588 -0.529 0.059 0.084 0.031 -0.027 0.433 0.279 -0.002 -0.17 -0.102 -0.42 -0.169 -0.31 -0.468 0.324 -0.17 0.428 0.087 -0.158 0.246 -0.058
silt 0.68 -0.471 -0.788 1 0.05 0.548 0.482 0.506 0.441 0.362 0.449 0.566 0.519 0.493 -0.054 -0.013 -0.068 -0.055 -0.409 -0.15 0.046 0.179 0.079 0.424 0.083 0.247 0.391 -0.196 0.175 -0.385 -0.18 0.119 -0.241 0.076
clay 0.023 0.099 -0.308 0.05 1 0.208 0.095 0.129 0.11 0.062 0.144 0.052 0.15 0.107 -0.098 -0.076 -0.044 0.02 -0.059 -0.02 0.025 0.015 0.02 0.006 0.012 0.241 0.238 -0.031 0.037 -0.096 -0.104 0.191 -0.046 0.066
arsenic 0.57 -0.127 -0.648 0.548 0.208 1 0.797 0.862 0.791 0.656 0.78 0.707 0.902 0.87 -0.266 -0.149 -0.193 0.008 -0.657 -0.067 0.06 0.216 0.076 0.66 0.214 0.522 0.709 -0.158 0.213 -0.444 -0.237 0.078 -0.466 0.181
cadmium 0.486 -0.23 -0.504 0.482 0.095 0.797 1 0.818 0.694 0.564 0.717 0.75 0.886 0.853 -0.308 -0.042 -0.291 -0.133 -0.783 -0.015 -0.002 0.186 -0.084 0.728 0.039 0.468 0.701 -0.14 0.142 -0.345 -0.306 -0.001 -0.46 0.111
chromium 0.606 -0.194 -0.587 0.506 0.129 0.862 0.818 1 0.909 0.818 0.917 0.753 0.92 0.939 -0.331 -0.167 -0.273 -0.041 -0.73 -0.02 0.263 0.437 0.103 0.733 0.344 0.596 0.763 -0.103 0.409 -0.323 -0.349 0.055 -0.559 0.362
copper 0.593 -0.23 -0.483 0.441 0.11 0.791 0.694 0.909 1 0.808 0.842 0.715 0.872 0.952 -0.298 -0.172 -0.225 -0.025 -0.655 0.238 0.438 0.571 0.219 0.752 0.432 0.641 0.755 0.169 0.536 -0.319 -0.451 0.033 -0.602 0.553
iron 0.586 -0.232 -0.407 0.362 0.062 0.656 0.564 0.818 0.808 1 0.878 0.461 0.664 0.785 -0.377 -0.273 -0.251 0.034 -0.616 0.114 0.508 0.652 0.325 0.671 0.624 0.578 0.674 0.061 0.644 -0.292 -0.368 0.055 -0.648 0.596
manganese 0.568 -0.199 -0.524 0.449 0.144 0.78 0.717 0.917 0.842 0.878 1 0.658 0.798 0.846 -0.287 -0.096 -0.261 -0.085 -0.758 -0.02 0.422 0.557 0.209 0.769 0.497 0.671 0.822 -0.082 0.562 -0.301 -0.466 0.106 -0.649 0.493
mercury 0.537 -0.207 -0.611 0.566 0.052 0.707 0.75 0.753 0.715 0.461 0.658 1 0.845 0.755 -0.234 -0.084 -0.199 -0.075 -0.724 -0.064 0.053 0.237 -0.043 0.731 0.133 0.509 0.703 -0.142 0.196 -0.356 -0.314 0.01 -0.42 0.168
lead 0.587 -0.169 -0.588 0.519 0.15 0.902 0.886 0.92 0.872 0.664 0.798 0.845 1 0.939 -0.304 -0.135 -0.252 -0.051 -0.707 0.029 0.129 0.316 0.05 0.739 0.211 0.599 0.769 -0.065 0.277 -0.376 -0.307 0.036 -0.475 0.275
zinc 0.605 -0.235 -0.529 0.493 0.107 0.87 0.853 0.939 0.952 0.785 0.846 0.755 0.939 1 -0.32 -0.145 -0.253 -0.056 -0.718 0.152 0.307 0.471 0.151 0.791 0.341 0.603 0.764 0.067 0.429 -0.359 -0.397 0.026 -0.578 0.431
S -0.026 0.029 0.059 -0.054 -0.098 -0.266 -0.308 -0.331 -0.298 -0.377 -0.287 -0.234 -0.304 -0.32 1 0.561 0.705 -0.052 0.348 -0.141 -0.113 -0.158 0.077 -0.255 -0.045 -0.315 -0.33 -0.069 -0.151 0.079 0.217 -0.112 0.335 -0.164
N -0.121 0.007 0.084 -0.013 -0.076 -0.149 -0.042 -0.167 -0.172 -0.273 -0.096 -0.084 -0.135 -0.145 0.561 1 -0.041 -0.683 -0.005 -0.061 -0.139 -0.163 -0.169 -0.023 -0.111 -0.116 -0.067 -0.061 -0.169 0.183 -0.008 -0.137 0.029 -0.133
H 0.122 0.012 0.031 -0.068 -0.044 -0.193 -0.291 -0.273 -0.225 -0.251 -0.261 -0.199 -0.252 -0.253 0.705 -0.041 1 0.598 0.373 -0.087 0.026 -0.014 0.285 -0.243 -0.028 -0.306 -0.328 -0.004 -0.015 -0.058 0.163 -0.035 0.425 -0.089
J 0.136 0.07 -0.027 -0.055 0.02 0.008 -0.133 -0.041 -0.025 0.034 -0.085 -0.075 -0.051 -0.056 -0.052 -0.683 0.598 1 0.186 0.01 0.073 0.054 0.236 -0.128 -0.021 -0.105 -0.146 0.034 0.061 -0.168 0.033 0.127 0.23 -0.014
aquaculture -0.41 0.143 0.433 -0.409 -0.059 -0.657 -0.783 -0.73 -0.655 -0.616 -0.758 -0.724 -0.707 -0.718 0.348 -0.005 0.373 0.186 1 -0.069 -0.168 -0.306 0.128 -0.827 -0.183 -0.597 -0.839 0.079 -0.271 0.282 0.594 0.02 0.722 -0.233
city -0.033 -0.068 0.279 -0.15 -0.02 -0.067 -0.015 -0.02 0.238 0.114 -0.02 -0.064 0.029 0.152 -0.141 -0.061 -0.087 0.01 -0.069 1 0.292 0.369 0.051 0.299 0.133 0.324 0.162 0.969 0.255 -0.097 -0.401 -0.012 -0.424 0.564
dredging_collect 0.22 -0.175 -0.002 0.046 0.025 0.06 -0.002 0.263 0.438 0.508 0.422 0.053 0.129 0.307 -0.113 -0.139 0.026 0.073 -0.168 0.292 1 0.895 0.734 0.359 0.741 0.485 0.416 0.371 0.946 0.012 -0.507 0.028 -0.366 0.849
dredging_dump 0.43 -0.161 -0.17 0.179 0.015 0.216 0.186 0.437 0.571 0.652 0.557 0.237 0.316 0.471 -0.158 -0.163 -0.014 0.054 -0.306 0.369 0.895 1 0.723 0.588 0.805 0.545 0.521 0.436 0.956 -0.173 -0.465 -0.048 -0.518 0.924
industry 0.309 -0.081 -0.102 0.079 0.02 0.076 -0.084 0.103 0.219 0.325 0.209 -0.043 0.05 0.151 0.077 -0.169 0.285 0.236 0.128 0.051 0.734 0.723 1 0.183 0.656 0.17 0.146 0.17 0.765 -0.172 -0.09 -0.086 -0.041 0.61
shipping_mooring 0.518 -0.216 -0.42 0.424 0.006 0.66 0.728 0.733 0.752 0.671 0.769 0.731 0.739 0.791 -0.255 -0.023 -0.243 -0.128 -0.827 0.299 0.359 0.588 0.183 1 0.41 0.592 0.766 0.24 0.5 -0.417 -0.597 -0.05 -0.728 0.543
shipping_traffic 0.291 -0.02 -0.169 0.083 0.012 0.214 0.039 0.344 0.432 0.624 0.497 0.133 0.211 0.341 -0.045 -0.111 -0.028 -0.021 -0.183 0.133 0.741 0.805 0.656 0.41 1 0.568 0.451 0.232 0.834 -0.005 -0.181 0.097 -0.521 0.825
sewers_rain 0.239 0 -0.31 0.247 0.241 0.522 0.468 0.596 0.641 0.578 0.671 0.509 0.599 0.603 -0.315 -0.116 -0.306 -0.105 -0.597 0.324 0.485 0.545 0.17 0.592 0.568 1 0.892 0.279 0.571 -0.07 -0.509 0.209 -0.747 0.661
sewers_waste 0.401 -0.073 -0.468 0.391 0.238 0.709 0.701 0.763 0.755 0.674 0.822 0.703 0.769 0.764 -0.33 -0.067 -0.328 -0.146 -0.839 0.162 0.416 0.521 0.146 0.766 0.451 0.892 1 0.069 0.523 -0.257 -0.569 0.061 -0.75 0.522
wharves_city -0.073 -0.061 0.324 -0.196 -0.031 -0.158 -0.14 -0.103 0.169 0.061 -0.082 -0.142 -0.065 0.067 -0.069 -0.061 -0.004 0.034 0.079 0.969 0.371 0.436 0.17 0.24 0.232 0.279 0.069 1 0.331 -0.042 -0.34 0.016 -0.35 0.632
wharves_industry 0.366 -0.166 -0.17 0.175 0.037 0.213 0.142 0.409 0.536 0.644 0.562 0.196 0.277 0.429 -0.151 -0.169 -0.015 0.061 -0.271 0.255 0.946 0.956 0.765 0.5 0.834 0.571 0.523 0.331 1 -0.094 -0.454 0.037 -0.497 0.9
fisheries_trap -0.508 0.16 0.428 -0.385 -0.096 -0.444 -0.345 -0.323 -0.319 -0.292 -0.301 -0.356 -0.376 -0.359 0.079 0.183 -0.058 -0.168 0.282 -0.097 0.012 -0.173 -0.172 -0.417 -0.005 -0.07 -0.257 -0.042 -0.094 1 0.226 0.132 0.145 -0.075
fisheries_trawl -0.213 0.172 0.087 -0.18 -0.104 -0.237 -0.306 -0.349 -0.451 -0.368 -0.466 -0.314 -0.307 -0.397 0.217 -0.008 0.163 0.033 0.594 -0.401 -0.507 -0.465 -0.09 -0.597 -0.181 -0.509 -0.569 -0.34 -0.454 0.226 1 -0.071 0.513 -0.458
fisheries_net 0.004 -0.055 -0.158 0.119 0.191 0.078 -0.001 0.055 0.033 0.055 0.106 0.01 0.036 0.026 -0.112 -0.137 -0.035 0.127 0.02 -0.012 0.028 -0.048 -0.086 -0.05 0.097 0.209 0.061 0.016 0.037 0.132 -0.071 1 -0.08 0.077
fisheries_dredge -0.238 0.068 0.246 -0.241 -0.046 -0.466 -0.46 -0.559 -0.602 -0.648 -0.649 -0.42 -0.475 -0.578 0.335 0.029 0.425 0.23 0.722 -0.424 -0.366 -0.518 -0.041 -0.728 -0.521 -0.747 -0.75 -0.35 -0.497 0.145 0.513 -0.08 1 -0.617
cumulative_influence 0.274 -0.12 -0.058 0.076 0.066 0.181 0.111 0.362 0.553 0.596 0.493 0.168 0.275 0.431 -0.164 -0.133 -0.089 -0.014 -0.233 0.564 0.849 0.924 0.61 0.543 0.825 0.661 0.522 0.632 0.9 -0.075 -0.458 0.077 -0.617 1

Several types of models were considered to explore relationships between variables: linear, quadratic, exponential and logarithmic. The model with the highest \(R^{2}\) is presented on each plot. Only linear models were implemented, as there are some bugs with the calculation of the others.

AquaInf

CityInf

InduInf

CollDred

DumpDred

MoorShip

TrafShip

RainSew

WastSew

CityWha

InduWha

TrapFish

TrawFish

NetFish

DredFish

Cumulative Influence

1.2. Species abundances by cumulative influence index

Let’s have a look at the distribution of species phyla along the gradient of cumulative influence.

Phylum mean abundances by group
Phylum low bad moderate high good
Annelida NA 29.5 32.3 19.7 NA
Arthropoda NA 20.3 50.6 26.3 NA
Cnidaria NA 0.1 0 0 NA
Echinodermata NA 13.5 1.32 5.12 NA
Mollusca NA 10.8 13.5 15.9 NA
Nematoda NA 22.7 9.95 0.0625 NA
Nemertea NA 0 0.195 0 NA
Sipuncula NA 0 0.268 0.438 NA

2. Species Distribution Models

The aim is to obtain models to predict the structure of benthic communities.

We will use abiotic parameters and the indices of influence (calculated in Section 1) as predictors, and we tested different methods: GLMs, GAMs, Random Forest and HMSC. Each method has been developed in dedicated scripts, whose final objects were imported here to present results and trends.

For each method, results are presented with a table, with McFadden’s R2 and variables coefficients, and maps, with the probability of presence of each taxon for which McFadden’s R2 is higher than 0.2 (and different than 1). The raster presents the results of the SDM (grey: low probability, dark blue: high). Stations are either plotted with colors (green = taxa present, red = taxon absent) or with circles (wider circcles = higher taxon density).

2.1. Generalized Linear Models

Presence/absence data

Here, we considered presence/absence data with a binomial distribution.

Abiotic parameters

McFadden’s R2, match ratios and variables coefficients for each taxon
  R2 MATCHED ERRORS intercept gravel sand silt clay arsenic cadmium chromium copper iron manganese mercury lead zinc
aceroides_aceroides_latipes 0.22 0 % 31.8 % -10.4 23.4 113 115 64.4 -0.266 0.0321 0.821 0.618 -2.36 0.464 0.686 -1.24 0.707
akanthophoreus_gracilis 0.21 4.5 % 45.5 % -1.89 9.04 18.6 19.2 7.8 1.75 -0.887 -0.0213 -0.0471 -0.922 -0.533 0.612 -0.174 -0.402
ameritella_agilis 0.5 0 % 13.6 % -10.8 30.9 62 62.8 38.9 1.83 5.99 13.6 -0.559 -3.94 -16.2 -0.879 -12.5 1.13
ameroculodes_edwardsi 0.43 0 % 13.6 % -293 -198 -403 -409 -1769 -3.19 2.53 5.25 6.01 -0.671 -14.8 -2.51 -2.95 -4.35
ampelisca_vadorum 1 0 % 4.5 % -67.7 -913 -1861 -1897 -1089 11.6 -41.1 140 -40.7 4.84 -66.9 5.55 64.1 -90.9
amphipoda 0.1 9.1 % 40.9 % -0.762 79.2 160 164 92.7 0.391 -0.168 1.47 -1.11 -0.499 -0.208 0.191 0.397 -0.184
anonyx_lilljeborgi 0.27 0 % 4.5 % -3.13 173 352 358 203 -0.668 -1.87 4.55 -3.78 -1.56 -0.271 0.326 0.415 1.32
anthozoa 0 0 % 4.5 % -26.6 -4.38e-15 8.66e-15 -2.48e-15 1.77e-14 -7.39e-15 -6.16e-15 5.86e-15 5.22e-15 -4.96e-15 1.41e-14 -1.85e-14 3.8e-14 -1.7e-14
arcteobia_anticostiensis 1 0 % 0 % -81 2746 5609 5720 3229 18.8 41.4 -89.5 30.3 10.8 -10.2 7.25 13.8 -29.7
arrhoges_occidentalis 1 0 % 9.1 % -64.1 -3128 -6321 -6469 -3628 35.2 8.03 77.8 9.24 -8.26 -12.7 14.4 -59.7 -62.4
astarte_sp 1 0 % 36.4 % -124 -9059 -18366 -18796 -10534 65.6 11.4 -157 187 -73.8 -6.71 54.2 -62.7 -32.2
axinopsida_orbiculata 0.17 0 % 36.4 % -361 -57.4 -117 -119 -2026 0.108 0.676 -0.997 0.817 0.0657 -0.204 -1.82 0.444 -0.52
axiothella_catenata 1 0 % 9.1 % -75.5 2279 4616 4712 2665 -7.45 -72.5 10.1 25.4 6.86 -40.7 1.25 153 -89.7
bathymedon_longimanus -4.54 4.5 % 0 % -2.81e+15 -4.41e+16 -8.98e+16 -9.15e+16 -5.17e+16 -2.17e+14 2.21e+14 -4.71e+15 -1.11e+15 -4.04e+14 1.84e+15 -5.11e+14 1.53e+15 2.47e+15
bathymedon_obtusifrons 1 0 % 9.1 % -108 5037 10216 10428 5883 7.54 49.7 85.8 58.3 -149 -3.7 -44.9 -5.72 -53.3
bipalponephtys_neotena 0.22 72.7 % 27.3 % 1.51 56.8 114 118 64.9 -0.572 0.318 -2.35 0.831 0.151 0.65 -0.166 0.806 0.0117
boreochiton_ruber 0.45 0 % 13.6 % -274 -238 -484 -494 -1717 -15 -8.01 -5.82 -12.1 -1.52 9.98 -4.63 12.9 11.8
brachydiastylis_sp 0.56 0 % 4.5 % -161 74.3 149 152 -723 -1.35 3.52 12.2 -0.564 0.494 -12.3 -2.37 -10.6 -0.395
byblis_gaimardii 0.41 0 % 9.1 % -258 -37.8 -77.7 -78.7 -1403 -8.28 -3.8 7.85 -5.59 0.0646 -4.26 -0.804 4.5 0.0173
cancer_irroratus 0.26 0 % 4.5 % -6.64 -84 -171 -175 -98.9 -2.38 0.808 1.02 -0.28 0.238 -1.32 -1.63 7.1 -4.77
caprella_septentrionalis 0.59 0 % 13.6 % -9.07 0.205 -1.01 -4.53 2.95 -2.87 5.48 2.11 8.67 -9.6 -1.33 -0.134 -0.0464 -4.48
chaetodermatida 0.19 0 % 31.8 % -3.62 -0.562 0.271 0.1 -7.55 -0.573 -1.74 -2.55 -0.362 -0.367 0.557 -0.234 2.56 1.31
chionoecetes_opilio 1 0 % 4.5 % -845 428 833 1144 -1503 -1.99 -676 -171 -568 -13.2 96.1 -346 332 757
chlamys_islandica 1 0 % 22.7 % -280 -32825 -66594 -67914 -38342 -251 -5.02 78.7 31.8 50.8 -70 60 97.3 -52.6
chone_sp 1 0 % 13.6 % -218 -907 -1547 -1642 -882 57.6 195 -91.3 447 -96.8 -113 28.7 -1.69 -373
ciliatocardium_ciliatum 1 0 % 18.2 % -240 -5301 -10686 -11057 -6039 -96.6 -291 76.4 -93 0.271 -79.5 87.9 283 52.4
cirripedia 1 0 % 9.1 % -37 573 1158 1179 674 3.33 6.14 2.25 -20.2 2.1 10.2 -2.42 -17 21.7
cistenides_granulata 0.25 0 % 22.7 % -2.7 28.8 58.5 59.5 30.9 -0.121 -2.12 0.382 -5.42 -0.164 0.572 -0.166 1.4 4.02
cossura_longocirrata 1 0 % 9.1 % -186 1986 3892 4100 2263 0.486 148 22.1 258 71.9 -165 29.1 -66.9 -250
crassicorophium_bonellii 0.56 0 % 4.5 % -248 13.8 32 32.3 -1298 -0.554 -2.53 -5.57 -2.24 -1.79 7.71 -3.37 4.06 1.81
crenella_decussata 0.63 0 % 18.2 % -11.1 -37.5 -77.9 -81.2 -41.6 -10.1 -5.28 -1.99 -7.15 -0.86 2.01 -4.01 8.6 6.16
cumacea 1 4.5 % 4.5 % -139 -12124 -24536 -25027 -14134 14.2 -82.9 117 37.7 3.9 -30.6 6.28 12.6 -50.9
cyclocardia_borealis 0 0 % 4.5 % -26.6 -4.38e-15 8.66e-15 -2.48e-15 1.77e-14 -7.39e-15 -6.16e-15 5.86e-15 5.22e-15 -4.96e-15 1.41e-14 -1.85e-14 3.8e-14 -1.7e-14
cyrtodaria_siliqua 1 0 % 9.1 % -160 -3200 -6419 -6557 -3753 -149 -234 -176 -283 -7.44 188 -60 262 339
diastylis_rathkei 0.31 0 % 13.6 % -4.27 -68.5 -140 -142 -80.9 -1.83 -0.0109 5.8 0.472 0.583 -1.54 -3.39 1.86 -4.77
diastylis_sculpta 0.6 0 % 18.2 % -18.3 27.3 58.1 58.8 34.9 4.61 4.2 13.3 29.3 -0.688 -26.7 -19.3 5.07 -30.9
diastylis_sp 1 0 % 13.6 % -1399 11977 23883 25131 13385 -2723 -515 380 -1140 202 286 -428 1086 823
echinarachnius_parma 0.73 4.5 % 31.8 % -30.8 -270 -549 -558 -306 -48.9 -6.46 11.6 -22.3 1.97 -11.7 -1.84 -4.49 29.7
edotia_montosa 1 0 % 9.1 % -123 -1456 -2914 -3059 -1626 54.1 41.2 4.47 64.1 -49.6 0.312 -22.1 -110 29.9
ennucula_tenuis 0.33 27.3 % 45.5 % -0.566 9.59 18.3 19.8 8.76 1.39 -2.45 -4.23 -0.882 0.0983 0.237 0.639 0.689 3.46
eteone_sp 0.19 0 % 0 % -329 -136 -276 -281 -1937 0.0678 -2.76 2.93 -1.27 -0.237 -1.13 -0.264 2.84 -1.2
euchone_sp 1 0 % 4.5 % -108 5037 10216 10428 5883 7.54 49.7 85.8 58.3 -149 -3.7 -44.9 -5.72 -53.3
eudorella_emarginata 0.44 0 % 4.5 % -209 18.9 34.6 38.7 -1082 -0.0695 2.71 3.75 4.27 0.918 -3.85 1.11 1.46 -8.42
eudorellopsis_integra 0.33 36.4 % 54.5 % -6.88 15.5 31.3 33 -22.6 1.37 -0.617 0.385 -1.01 -0.764 1.03 1.12 -2.59 1.62
euspira_pallida -5.62 0 % 4.5 % -2.7e+15 -1.94e+17 -3.94e+17 -4.01e+17 -2.28e+17 -2.45e+14 -4.43e+14 -1.64e+15 -5.51e+14 7.79e+13 1.11e+15 -1.29e+14 1.41e+15 7.59e+14
glycera_capitata 1 0 % 9.1 % -86.1 -5103 -10385 -10614 -5948 20.8 66 -39.5 156 10.9 -45.8 -10.9 -16.4 -118
glycera_sp 0.58 0 % 18.2 % -9.01 -330 -671 -684 -387 -0.98 1.13 11.8 -3.05 -14.4 0.545 -2.13 0.385 2.34
goniada_maculata 0.21 13.6 % 40.9 % -371 9.67 21.6 22.6 -2010 0.459 -0.34 -0.325 -1.14 -0.0191 -0.293 0.185 -0.01 0.69
guernea_prinassus_nordenskioldi 0 0 % 9.1 % -26.6 -4.38e-15 8.66e-15 -2.48e-15 1.77e-14 -7.39e-15 -6.16e-15 5.86e-15 5.22e-15 -4.96e-15 1.41e-14 -1.85e-14 3.8e-14 -1.7e-14
halacaridae_spp 1 0 % 22.7 % -280 -32825 -66594 -67914 -38342 -251 -5.02 78.7 31.8 50.8 -70 60 97.3 -52.6
haminoea_solitaria 0.43 0 % 9.1 % -39.7 -12.2 6.91 6.44 -42.7 12.7 16.8 8.05 35.8 -0.334 -31.7 -16.2 -4.63 -46.7
hardametopa_carinata 1 0 % 4.5 % -108 5037 10216 10428 5883 7.54 49.7 85.8 58.3 -149 -3.7 -44.9 -5.72 -53.3
harmothoe_sp 0.31 0 % 4.5 % -273 -106 -218 -221 -1586 -0.408 0.394 1.72 3.12 -0.0624 -0.388 -3.07 0.0219 -3.21
harpacticoida 0.22 18.2 % 68.2 % -0.0818 54.9 112 113 64.9 0.752 2.73 2.23 5.9 -0.0947 -2.51 1.78 -2.39 -7.31
hediste_diversicolor 0.55 9.1 % 9.1 % -6.37 188 382 390 221 -13.9 0.353 -1.77 1.42 -1.05 7.15 -4.6 12.4 -6.54
heteranomia_squamula 1 0 % 4.5 % -53.8 1881 3809 3888 2196 -17.2 -13.4 -65 1.52 -0.673 40.4 -11.4 38.5 11.4
hiatella_arctica 1 4.5 % 22.7 % -295 -4490 -9132 -9373 -5150 -244 -135 -445 -182 -47.1 373 -170 321 237
holothuroidea 0.69 4.5 % 9.1 % -25.6 -158 -259 -269 -179 -13.7 -8.13 -11.1 -2.03 -3.01 12.5 -3.81 13.7 7.22
idotea_phosphorea 0.6 0 % 9.1 % -11 -462 -940 -959 -542 -9.8 -1.18 -9.1 -2.9 0.913 3.88 -9.09 22.3 -2.03
ischyroceridae_spp 1 0 % 9.1 % -108 5795 11763 12021 6814 8.21 -88.2 45 58.8 6.9 -56.5 26.9 -6.78 -14.9
ischyrocerus_anguipes 1 0 % 22.7 % -216 -8512 -17264 -17700 -9875 -11.1 140 130 184 -238 -29.6 47.9 -125 -57.9
isopoda 0 0 % 4.5 % -26.6 -4.38e-15 8.66e-15 -2.48e-15 1.77e-14 -7.39e-15 -6.16e-15 5.86e-15 5.22e-15 -4.96e-15 1.41e-14 -1.85e-14 3.8e-14 -1.7e-14
lacuna_vincta 0.26 0 % 9.1 % -6.64 -84 -171 -175 -98.9 -2.38 0.808 1.02 -0.28 0.238 -1.32 -1.63 7.1 -4.77
lamprops_fuscatus 0.2 0 % 13.6 % -2.85 -11.9 -22.5 -23.4 -13.3 -1.7 0.801 -1.22 3.36 0.122 0.811 -0.0254 0.149 -3.4
lamprops_quadriplicata 1 0 % 13.6 % -59.5 -873 -1720 -1781 -977 19.4 13.9 -0.315 25.5 -4.94 17.8 2.95 43 -102
lepeta_caeca 0.65 0 % 9.1 % -324 -1717 -3491 -3561 -3653 -36.1 -2.18 -15 5.42 0.695 9.57 -13.2 33.9 -7.38
leucon_leucon_nasicoides 0.23 13.6 % 54.5 % -342 61.5 125 128 -1790 -0.155 -1.3 0.0817 -1.7 -0.0152 0.654 0.292 1.22 0.889
littorina_littorea 1 0 % 18.2 % -312 -30048 -61020 -62243 -35134 -456 -349 -43.4 -723 -11.8 122 -233 788 712
lumbrineridae_spp 1 0 % 13.6 % -1412 5646 11068 11995 6035 -2776 -335 351 -1062 191 242 -431 891 793
lysianassidae_spp 1 0 % 4.5 % -358 -5020 -10079 -10215 -5731 -526 -27.3 154 -142 30.1 -139 -160 169 82.8
macoma_calcarea 0.15 72.7 % 22.7 % 1.36 -8.33 -16.9 -16.4 -10.8 0.244 1.18 -1.19 2.93 0.148 -0.0685 0.102 -0.768 -3.22
maera_danae 1 0 % 13.6 % -218 -907 -1547 -1642 -882 57.6 195 -91.3 447 -96.8 -113 28.7 -1.69 -373
maldane_sarsi -10.38 0 % 4.5 % -2.15e+15 1.27e+16 2.54e+16 2.7e+16 1.31e+16 -4.3e+14 -5.45e+14 7.28e+13 1.52e+15 -2.73e+14 1.44e+14 -1.01e+15 1.17e+15 -1.24e+15
maldanidae_spp 0.18 0 % 27.3 % -9.35 -44.3 -30.7 -30.7 -18.8 -0.307 -0.531 0.38 0.942 -0.0827 -0.516 0.342 0.695 -1.12
monoculopsis_longicornis 1 4.5 % 27.3 % -116 -7503 -15207 -15552 -8722 29.1 -114 -133 -8.02 -82.2 25.7 32.7 11.1 200
muculus_musculus_discors 1 0 % 22.7 % -280 -32825 -66594 -67914 -38342 -251 -5.02 78.7 31.8 50.8 -70 60 97.3 -52.6
mytilus_sp 0.35 4.5 % 9.1 % -4.33 -16.1 -32.9 -32.7 -20.6 -4.73 -0.194 -2.37 4.79 -0.74 0.273 -5.71 8.64 -5.53
nematoda 0.47 27.3 % 27.3 % -2.24 28 58 57.8 24 0.672 -2.36 0.722 -4.3 -2.82 2.01 0.0213 0.941 2.95
nemertea 1 0 % 13.6 % -78.5 -2643 -5401 -5524 -3089 24.4 71 -34 147 13 -63.1 13.3 -47.5 -104
neoleanira_tetragona 1 0 % 9.1 % -49.8 -409 -754 -789 -425 14 19.8 46.6 26.4 0.618 -26.4 9.1 22 -98.4
nephtyidae_spp 0.3 4.5 % 13.6 % -135 -50.9 -36.5 -37.2 -683 1.44 -0.454 3.58 -2.55 -7.47 2.63 0.12 -1.04 1.95
nephtys_caeca 0.66 0 % 4.5 % -274 341 689 700 -1055 4.27 11.4 12.1 11.6 1.63 -9.11 -0.933 -11.9 -17.6
nephtys_incisa 0.2 0 % 45.5 % -1.35 -60.2 -123 -124 -72.3 0.0295 -2.44 -0.223 -0.594 -0.579 0.0233 -0.349 1.6 0.871
nephtys_sp 0.24 0 % 0 % -137 201 471 480 -401 -0.678 -1.71 -3.81 -1.21 -0.0774 1.08 -1.11 5.06 1.36
nuculana_minuta 0.17 0 % 13.6 % -335 -3.35 -7.37 -6.74 -1814 -1.58 -1.28 -0.641 -0.741 -0.482 1.08 -1.05 2.11 0.0332
nymphonidae_spp 1 0 % 4.5 % -53.8 1881 3809 3888 2196 -17.2 -13.4 -65 1.52 -0.673 40.4 -11.4 38.5 11.4
oenopota_sp 0.45 0 % 18.2 % -5.13 105 213 218 122 0.882 1.89 -2.36 10.8 -1.54 1.55 -1.16 2.12 -14.6
oligochaeta 0.45 0 % 22.7 % -120 -48.1 -63.1 -62.9 -638 0.284 3.83 2.25 6.68 -0.0049 -2.29 2.72 -9.28 -1.56
ophelia_limacina 0.14 0 % 9.1 % -341 47.2 94.8 96.6 -1786 0.322 -0.0349 -0.66 0.476 0.0997 -1.23 0.605 0.683 -0.285
opheliidae_spp -2.79 0 % 4.5 % -3.32e+15 -7.34e+16 -1.5e+17 -1.52e+17 -8.76e+16 -6.15e+14 -5.45e+14 2.03e+15 -3.8e+15 3.95e+13 -5.09e+14 -1.27e+15 2.03e+15 6.02e+14
ophiopholis_aculeata 1 0 % 0 % -664 -34711 -70638 -71718 -41205 -563 -20 446 -117 68.7 -207 -262 -142 111
ophiura_robusta 0.49 0 % 13.6 % -307 -45.3 -91.3 -94.4 -1685 -5.84 -3.48 -3.79 -3.08 -1.3 5.96 -1.9 5.23 2
orchomenella_minuta 1 0 % 18.2 % -124 199 342 427 57.2 -32.7 -59.1 21.3 48.8 8.07 -7.44 -30.5 -1.88 -1.54
ostracoda 0.25 13.6 % 50 % -1.77 -28.8 -56.8 -57.5 -34.2 0.55 -1.03 -3.08 0.892 -1.07 0.38 -0.207 0.0732 2.11
pagurus_sp 1 0 % 0 % -81 2746 5609 5720 3229 18.8 41.4 -89.5 30.3 10.8 -10.2 7.25 13.8 -29.7
pagurus_pubescens 1 0 % 18.2 % -595 -9864 -20064 -20566 -11548 -818 -459 -800 -609 -180 873 -339 876 759
pandalus_montagui 1 0 % 4.5 % -33.4 -90.4 -174 -175 -99.6 -12.2 -16.7 -9.66 -5.77 -1.59 17.1 3.92 12.6 8.6
parathyasira_equalis 0.43 0 % 9.1 % -39.7 -12.2 6.91 6.44 -42.7 12.7 16.8 8.05 35.8 -0.334 -31.7 -16.2 -4.63 -46.7
parvicardium_pinnulatum 0.33 0 % 9.1 % -8.77 7.8 16 16.7 10.4 -0.45 2.39 7.5 7.35 -0.449 -11.7 -4.85 0.561 -10.6
periploma_leanum 0.39 0 % 4.5 % -138 272 607 619 -331 -0.612 2.61 -6.26 4.04 -1.33 1.09 0.354 4.04 -1.91
philine_lima 1 0 % 0 % -81 2746 5609 5720 3229 18.8 41.4 -89.5 30.3 10.8 -10.2 7.25 13.8 -29.7
philomedes_sp 0.35 0 % 0 % -314 -9.24 -19.3 -20.3 -1695 1.76 0.78 4.69 -0.0408 -0.179 -4.02 -0.307 -4.69 -0.465
pholoe_longa 1 0 % 4.5 % -108 5037 10216 10428 5883 7.54 49.7 85.8 58.3 -149 -3.7 -44.9 -5.72 -53.3
pholoe_sp 0.21 40.9 % 27.3 % -0.639 12.9 25.9 27.4 13 -2.7 -1.66 -3.85 -0.444 -0.644 3.21 -1.07 2.11 2.91
phoxocephalus_holbolli 0.3 9.1 % 22.7 % -2.33 -7.78 -15.2 -16 -7.38 -4.61 -2.33 -0.239 -6.42 -1.16 2.55 -0.475 2.81 6.63
polynoidae_spp 0.14 0 % 36.4 % -1.47 8.13 17.2 18.3 8.32 -0.738 -1.28 0.377 -1.77 -0.419 0.373 0.124 1.17 1.13
pontogeneia_inermis 1 0 % 13.6 % -53.2 -2217 -4498 -4582 -2587 14.5 2.58 104 36.7 4.47 -70.2 15 -26.8 -82.6
pontoporeia_femorata 0.42 13.6 % 27.3 % -339 -67.7 -139 -140 -1917 -1.52 2.19 -0.0403 4.63 0.559 -0.252 -0.123 0.121 -4.43
praxillella_praetermissa 0.44 0 % 4.5 % -11.9 279 621 634 355 -0.287 2.71 -6.93 4.68 0.635 1.79 0.0171 3.73 -4.19
propebela_turricula 0.29 0 % 13.6 % -134 -87.4 -109 -111 -723 -1.09 -5.1 2.6 -2.16 -0.692 0.0859 -1.34 7.55 -2.16
protomedeia_fasciata 0.32 4.5 % 18.2 % -278 20.3 39.4 42 -1470 -5.75 -1.04 -0.188 -2.74 -0.971 3.1 -1.01 -0.387 4.94
protomedeia_grandimana 0.3 13.6 % 50 % -2.32 96.5 195 200 101 -1.4 -0.929 0.163 2.52 -0.154 -0.31 0.847 2.33 -3.31
puncturella_noachina 1 0 % 13.6 % -78.5 -2643 -5401 -5524 -3089 24.4 71 -34 147 13 -63.1 13.3 -47.5 -104
quasimelita_formosa 0.16 0 % 27.3 % -1.86 17.1 34.3 36.1 17.7 0.00508 -0.103 0.932 2.78 0.115 -2.56 -0.173 0.724 -3.24
quasimelita_quadrispinosa 1 0 % 9.1 % -108 5795 11763 12021 6814 8.21 -88.2 45 58.8 6.9 -56.5 26.9 -6.78 -14.9
retusa_obtusa 1 0 % 27.3 % -87.2 -1353 -2734 -2818 -1550 -8.83 71.5 8.83 118 -29.8 -4.38 33.3 -137 -1.42
sabellidae_spp 0.35 0 % 18.2 % -10.6 -109 -163 -167 -92.4 -0.686 1.46 2.3 -0.102 -0.894 0.231 0.954 -1.83 -0.323
scoletoma_fragilis -10.34 4.5 % 27.3 % -2.15e+15 5.76e+15 1.13e+16 1.23e+16 7.32e+15 -5.57e+14 1.05e+15 2.29e+15 2.23e+15 -1.27e+14 -8.31e+14 -6.63e+14 4.84e+14 -3.53e+15
scoletoma_sp 0.44 0 % 0 % -24.1 -458 -896 -913 -566 4.33 4.4 8.55 2.1 1.1 -11.4 -0.561 -14.5 0.741
scoloplos_sp 0 0 % 4.5 % -26.6 -4.38e-15 8.66e-15 -2.48e-15 1.77e-14 -7.39e-15 -6.16e-15 5.86e-15 5.22e-15 -4.96e-15 1.41e-14 -1.85e-14 3.8e-14 -1.7e-14
serripes_groenlandicus 1 0 % 9.1 % -187 -19059 -38750 -39489 -22326 14.8 84.5 5.62 260 36.4 -76.4 -27.3 -63.3 -165
sipuncula 0.27 0 % 13.6 % -10.9 105 270 277 155 -0.458 -0.0682 -2.67 -0.0657 -1.6 1.47 -0.787 0.383 2.58
solamen_glandula 0 0 % 4.5 % -26.6 -4.38e-15 8.66e-15 -2.48e-15 1.77e-14 -7.39e-15 -6.16e-15 5.86e-15 5.22e-15 -4.96e-15 1.41e-14 -1.85e-14 3.8e-14 -1.7e-14
solariella_sp 0.61 0 % 9.1 % -13.7 -80.9 -166 -166 -113 -3.18 -6.97 0.766 -6.67 -2.2 -2.25 -6.05 3.1 8.71
strongylocentrotus_sp -6.59 0 % 4.5 % -3.2e+15 -2.59e+17 -5.27e+17 -5.37e+17 -3.04e+17 2.45e+14 -8.64e+14 1.84e+15 -1.2e+14 -1.18e+14 -8.88e+14 -6.81e+14 -1.87e+13 -3.57e+14
tachyrhynchus_erosus 0 0 % 4.5 % -26.6 -4.38e-15 8.66e-15 -2.48e-15 1.77e-14 -7.39e-15 -6.16e-15 5.86e-15 5.22e-15 -4.96e-15 1.41e-14 -1.85e-14 3.8e-14 -1.7e-14
thracia_septentrionalis 0.18 0 % 18.2 % -1.69 128 260 265 151 -0.237 0.15 -2.23 -0.782 -0.366 1.36 -0.965 0.924 1.16
thyasira_gouldi 0.17 0 % 45.5 % -2.38 1.31 2.66 3.51 -5.31 -0.5 -2.42 -0.594 -1.72 -1.1 1.07 -0.289 1.06 2.57
thyasira_sp 0 0 % 4.5 % -26.6 -4.38e-15 8.66e-15 -2.48e-15 1.77e-14 -7.39e-15 -6.16e-15 5.86e-15 5.22e-15 -4.96e-15 1.41e-14 -1.85e-14 3.8e-14 -1.7e-14
trichotropis_bicarinata 0.25 0 % 0 % -68 -20.7 11.4 12.1 -279 3.19 5.08 4.23 7.3 0.22 -8.59 -1.64 -8.21 -6.9
turritellopsis_stimpsoni 0.56 4.5 % 9.1 % -311 -262 -530 -545 -1946 3.3 -5.9 4.67 9.33 -1.22 -8.37 3.16 7.1 -15
yoldia_myalis 0.08 0 % 0 % -356 55.1 112 113 -1861 -0.113 -0.381 0.224 -0.622 -0.137 0.285 -0.0277 1.19 -0.582

Prediction of specific richness based on this model:

Influence indices

McFadden’s R2, match ratios and variables coefficients for each taxon
  R2 MATCHED ERRORS intercept city dredging_collect dredging_dump industry shipping_mooring shipping_traffic sewers_rain sewers_waste wharves_city wharves_industry fisheries_trap fisheries_trawl fisheries_net fisheries_dredge
aceroides_aceroides_latipes 0.29 4.5 % 36.4 % -2.1 -1.13 3.47 5.33 0.32 1.24 3.04 -2.7 1.95 0.709 -12.2 0.321 -1.97 -1.24 1.78
akanthophoreus_gracilis 0.4 22.7 % 18.2 % -46 -1.77 0.949 -3.62 3.5 -0.0852 2.26 -4.49 5.21 2.68 -2.35 -0.0308 0.0186 -454 1.75
ameritella_agilis 0.66 0 % 18.2 % -11.8 -20.9 2.65 23.8 -4.45 2.27 -9.58 14.4 -7.19 9.97 -25.6 0.948 0.999 -1.05 1.64
ameroculodes_edwardsi -15.34 0 % 9.1 % -1.86e+15 2.52e+15 -4.33e+14 -1.81e+15 2.15e+15 -6.34e+14 9.37e+14 -6.4e+14 3.69e+14 -2.35e+15 6.25e+14 -6.6e+14 -4.21e+14 -1.89e+14 6.19e+14
ampelisca_vadorum 1 0 % 4.5 % -44.1 -14.7 4.89 1.15 -11 -17.7 16.4 -45.2 52.6 20.5 -10.8 -35.4 1.11 3.41 -2.01
amphipoda 0.21 9.1 % 40.9 % -43.2 4.38 1.19 4.1 1.82 -0.0518 0.457 0.31 0.223 -5.11 -6.61 0.434 0.105 -438 0.267
anonyx_lilljeborgi 0.34 0 % 9.1 % -50.9 -8.94 -2.9 2.36 -1.6 -0.0344 2.85 -1.51 -0.833 7.86 -1.79 -0.081 -8.32 -479 -2.31
anthozoa 0 0 % 4.5 % -26.6 -2.33e-14 -3.96e-14 -6.51e-14 3.04e-15 -1.61e-14 -1.36e-14 -2.49e-14 4.32e-14 4.04e-14 1.1e-13 1.1e-15 1.9e-15 7.81e-16 1.32e-15
arcteobia_anticostiensis 1 0 % 4.5 % -116 -59.1 -150 -27.3 -12.7 -21.3 -16.8 -0.26 32.3 90.1 168 -139 -103 4.06 43.7
arrhoges_occidentalis 1 0 % 0 % -62.2 -86.4 21.9 46.5 16.6 -62.6 -17.6 -112 174 97.4 -87.9 0.123 6.79 11.4 -25.2
astarte_sp 1 4.5 % 18.2 % -297 1535 959 174 180 559 439 540 -1049 -1712 -1348 -31.8 6.79 22.1 92.1
axinopsida_orbiculata 0.34 0 % 36.4 % -4.2 10.1 -5.86 4.56 1.79 -3.44 1.39 -11.5 9.09 -7.31 1.74 0.589 1.18 0.111 -1.78
axiothella_catenata 1 0 % 9.1 % -155 419 -209 365 -55.2 39.1 115 -86.2 -61.7 -442 -74.6 3.43 11.3 39 113
bathymedon_longimanus 1 0 % 9.1 % -186 27.5 -286 402 -292 -91.1 -115 15.1 -126 -113 343 -10.7 -53.9 26.2 57.8
bathymedon_obtusifrons 1 0 % 18.2 % -105 -379 -49.5 30.9 89.5 -32.5 -104 44.4 139 409 -150 -5.97 -0.224 1.01 -14.7
bipalponephtys_neotena 0.27 90.9 % 9.1 % 76.3 -0.966 0.999 1.68 2.37 0.577 0.652 -1.5 3.09 1.37 -5.72 0.586 -0.179 770 1.21
boreochiton_ruber 1 0 % 13.6 % -359 1458 240 92.3 -77 266 124 730 -1415 -1809 57.8 -11.6 5.11 15.9 32.8
brachydiastylis_sp 1 0 % 9.1 % -42.3 9.84 15.5 13.4 -13.3 -2.46 24.6 -31.3 29.5 -8.9 -33.6 -33.4 2.48 3.45 16.7
byblis_gaimardii 1 4.5 % 4.5 % -121 -8.48 -54.7 -58.4 -9.3 -42.2 60.2 -23.4 63.5 35.1 54.7 -234 -2.18 4.06 49.8
cancer_irroratus 1 0 % 22.7 % -354 193 -124 35.5 -421 368 256 108 -67.5 -171 244 12.4 132 16.8 494
caprella_septentrionalis -8.94 0 % 22.7 % -1.57e+15 -2.4e+15 -4.35e+14 2.59e+15 -2.55e+14 -1.42e+14 -1.08e+15 2.15e+15 -5.38e+14 2.49e+15 -2.99e+15 -3.51e+14 -2.09e+14 -4.32e+14 -2.03e+14
chaetodermatida 0.23 0 % 36.4 % -71.7 -2.06 2.7 -1.93 1.83 0.0827 0.499 1.64 -0.854 3.43 -4.47 -0.581 -0.0342 -717 -0.0841
chionoecetes_opilio 1 0 % 18.2 % -241 88.6 228 953 191 164 -116 641 -715 -308 -1250 22.9 -171 7.07 -207
chlamys_islandica 1 0 % 0 % -34.1 7.84 -4.84 -7.48 4.72 -5.51 -18.2 -25 28.6 -0.0706 30.4 0.38 11 4.11 0.614
chone_sp 1 0 % 0 % -65.2 -149 1.37 -27.2 69.1 -21.2 -64.5 24.9 81.2 175 -67.5 7.09 4.04 1.05 0.956
ciliatocardium_ciliatum 1 0 % 4.5 % -61.6 -21.6 -118 120 -19.4 -58 -21.9 22.2 -7.3 6.59 42.5 -0.0955 -13.1 1.69 -63.4
cirripedia 1 0 % 0 % -55.9 32 67.1 -12.2 40.6 27.9 -6.86 40.9 -35.3 -63.6 -94 15.9 0.522 1.17 -18.7
cistenides_granulata 0.38 4.5 % 31.8 % -75.3 -20.8 -0.786 -8.48 -0.276 10.1 1.78 1.03 -11.7 16.2 8.93 1.03 0.125 -724 -0.527
cossura_longocirrata 1 0 % 18.2 % -68.8 -136 126 171 -0.218 142 -58.5 176 -239 44.9 -284 7.2 7.33 0.0651 -13.3
crassicorophium_bonellii 1 0 % 9.1 % -65.4 -88.6 -75 -82.3 -11.3 -105 -23.2 -220 316 158 183 -4.18 19.9 16.8 62.3
crenella_decussata 1 0 % 22.7 % -480 28.8 581 110 -276 1011 253 942 -2306 -684 -286 22.2 -25.9 -50.2 -66.6
cumacea 1 0 % 13.6 % -132 -48 75.5 -95 -18.4 -68.6 102 -111 166 87.6 -63.7 -0.24 -67.5 -1.34 -182
cyclocardia_borealis 0 0 % 4.5 % -26.6 -2.33e-14 -3.96e-14 -6.51e-14 3.04e-15 -1.61e-14 -1.36e-14 -2.49e-14 4.32e-14 4.04e-14 1.1e-13 1.1e-15 1.9e-15 7.81e-16 1.32e-15
cyrtodaria_siliqua 1 0 % 4.5 % -125 511 -138 84 13 61.6 83.9 114 -276 -560 106 -12.9 -2.63 13.7 42.8
diastylis_rathkei 0.21 0 % 13.6 % -45 0.101 -2.75 3.14 -1.92 -2.97 0.171 -2.21 0.716 -0.701 3.27 0.00195 -0.382 -429 -2.75
diastylis_sculpta -10.59 0 % 13.6 % -2.94e+15 -5.95e+15 -3e+15 -1.72e+15 -8.23e+14 -1.15e+15 -2.23e+15 -2.01e+15 1.76e+15 7.47e+15 6.6e+15 -9.76e+13 -1.17e+14 3.69e+14 -7.95e+14
diastylis_sp 1 0 % 0 % -104 61.7 -232 198 12.4 -28.8 -130 172 -166 -103 162 8.08 8.14 4.29 -98.2
echinarachnius_parma 0.56 9.1 % 13.6 % -66.7 8.45 2.84 5.36 -11.9 -0.128 -1.8 10.7 -25.1 -13 9.96 0.55 0.611 -603 -2.87
edotia_montosa 0.33 0 % 0 % -268 4.61 -5.15 -6.45 0.949 -2.34 0.672 -2.46 3.01 -3.11 11.2 -5.63 -590 -710 -112
ennucula_tenuis 0.39 40.9 % 27.3 % -0.106 -1.76 0.937 -2.92 2.71 0.31 1.62 -1.99 2.47 3.1 -1.48 -0.164 -0.0471 0.834 2.53
eteone_sp 1 0 % 13.6 % -1274 -705 -1370 -1229 202 -391 -71.4 -399 790 1475 1829 -26.8 -10.6 -8316 -326
euchone_sp 1 0 % 13.6 % -105 -379 -49.5 30.9 89.5 -32.5 -104 44.4 139 409 -150 -5.97 -0.224 1.01 -14.7
eudorella_emarginata 0.72 0 % 13.6 % -127 -85.4 133 47.7 5.3 71.6 29.7 -58.7 150 38 -279 -7.47 18.8 12.9 37.1
eudorellopsis_integra 0.84 68.2 % 22.7 % -15.3 -288 49.6 -42.3 17.8 82.8 18.8 -36.5 -3.29 255 -43.9 -0.754 -1.07 -1.35 9.52
euspira_pallida 1 0 % 4.5 % -256 -201 357 722 118 -29.4 24.7 350 -320 81.6 -1097 -59.7 -68.2 11.6 -12.2
glycera_capitata 1 0 % 9.1 % -68.1 63.2 63.2 -92.6 74.9 28.1 17 47.4 -34.6 -91.8 -71.4 6.98 -4.53 -0.45 -6.53
glycera_sp 1 4.5 % 4.5 % -737 -187 434 1868 -715 423 -1106 1117 -1623 -533 -623 -168 183 93.8 -211
goniada_maculata 0.46 22.7 % 40.9 % -9.31 -76.8 8.03 -11.8 -0.701 26.3 3.21 -1.21 -20.1 63.5 5.38 -0.208 1.76 0.935 1.9
guernea_prinassus_nordenskioldi 0 0 % 9.1 % -26.6 -2.33e-14 -3.96e-14 -6.51e-14 3.04e-15 -1.61e-14 -1.36e-14 -2.49e-14 4.32e-14 4.04e-14 1.1e-13 1.1e-15 1.9e-15 7.81e-16 1.32e-15
halacaridae_spp 1 0 % 0 % -34.1 7.84 -4.84 -7.48 4.72 -5.51 -18.2 -25 28.6 -0.0706 30.4 0.38 11 4.11 0.614
haminoea_solitaria 1 0 % 4.5 % -137 231 -386 -281 81.1 -24.7 6.45 -79.1 129 -112 592 -11.4 -12.5 16.4 155
hardametopa_carinata 1 0 % 13.6 % -105 -379 -49.5 30.9 89.5 -32.5 -104 44.4 139 409 -150 -5.97 -0.224 1.01 -14.7
harmothoe_sp 1 4.5 % 4.5 % -64.7 100 78.4 -38.2 64.1 46.3 32.8 52.8 -58.5 -125 -135 12.2 -1.39 6.3 2.77
harpacticoida 0.32 18.2 % 59.1 % -58.5 -0.274 5.17 -1.13 -0.344 0.885 1.77 -2.63 2.47 1.12 -6.09 0.186 0.0078 -606 -0.208
hediste_diversicolor 0.47 9.1 % 4.5 % -484 3.98 11.3 11.7 -1.31 3.59 -6.18 10.4 -13.6 -8.98 -13.5 -0.207 -1360 -654 -173
heteranomia_squamula 1 0 % 9.1 % -116 72.2 -19.5 58.3 -72 96.9 -21.5 181 -373 -162 106 19.7 1.69 0.641 -71.6
hiatella_arctica 1 4.5 % 4.5 % -373 1147 49.6 587 -320 290 -21.7 1031 -1770 -1581 41.3 -0.942 -153 -2.88 -56.3
holothuroidea 1 9.1 % 4.5 % -107 201 146 -251 10.6 49.2 126 -114 79.2 -143 22.2 16.4 15.8 9.52 42.6
idotea_phosphorea 1 0 % 4.5 % -499 30.9 271 683 -690 289 -159 943 -1612 -248 -330 6.38 12.1 2.05 -52.2
ischyroceridae_spp 1 0 % 13.6 % -98.3 -340 162 83.2 -61.1 154 9.94 37.7 -163 246 -197 -4.03 10.6 3.64 -29.9
ischyrocerus_anguipes 1 0 % 9.1 % -194 -245 -146 -6.3 -113 -180 -8.61 -395 473 339 177 -179 -44.8 35.5 -17.7
isopoda 0 0 % 4.5 % -26.6 -2.33e-14 -3.96e-14 -6.51e-14 3.04e-15 -1.61e-14 -1.36e-14 -2.49e-14 4.32e-14 4.04e-14 1.1e-13 1.1e-15 1.9e-15 7.81e-16 1.32e-15
lacuna_vincta 1 0 % 27.3 % -354 193 -124 35.5 -421 368 256 108 -67.5 -171 244 12.4 132 16.8 494
lamprops_fuscatus 0.24 4.5 % 13.6 % -64.3 2.37 -0.826 -2.34 0.361 0.499 2.2 -1.06 -0.894 -2.01 2.15 0.395 -6.49 -628 0.88
lamprops_quadriplicata 1 0 % 22.7 % -282 -568 389 137 -80.1 228 -92.4 219 116 432 -631 -24.7 75.3 1.13 134
lepeta_caeca 1 0 % 18.2 % -743 1258 329 -799 111 346 248 752 -1577 -932 -20.4 -101 -14.4 30.6 39.7
leucon_leucon_nasicoides 0.36 40.9 % 31.8 % -3.24 -18.5 4.27 1.39 0.0507 11.2 0.716 6.73 -14.7 12.2 -5.29 -1.98 -0.0179 0.473 0.705
littorina_littorea -4.54 0 % 9.1 % -2.37e+15 4.22e+14 -1.47e+14 2.61e+15 -2.58e+15 -1.13e+15 5.47e+13 -4.28e+14 -9.98e+14 -9.61e+14 1.19e+14 -2.4e+14 -7.08e+14 2.29e+14 -1.78e+15
lumbrineridae_spp 1 0 % 9.1 % -144 216 -29.4 334 49.9 48.5 -167 431 -476 -366 -138 33.3 9.65 0.0224 -91.1
lysianassidae_spp 1 0 % 4.5 % -115 180 -35.2 -154 -45.2 -33.5 0.635 -57.6 -41.6 -173 292 15.9 8.67 13.3 2.14
macoma_calcarea 0.2 72.7 % 27.3 % 2 2.01 6.28 3.19 0.591 1.74 0.674 1.41 -2.98 -2.93 -9.41 -0.213 0.134 0.608 0.814
maera_danae 1 0 % 0 % -65.2 -149 1.37 -27.2 69.1 -21.2 -64.5 24.9 81.2 175 -67.5 7.09 4.04 1.05 0.956
maldane_sarsi 1 0 % 4.5 % -76.3 -76.7 -305 -10.7 11.9 -79.6 -30 -16.2 108 137 286 -2.62 -8.29 6.63 -3.93
maldanidae_spp 0.29 9.1 % 31.8 % -80.3 -21 3.64 -1.16 0.767 8.62 -0.172 4.72 -8.72 17.2 -4.5 0.207 -0.0326 -806 0.133
monoculopsis_longicornis 1 4.5 % 13.6 % -154 133 553 496 49.8 83.6 68.5 299 -279 -247 -1097 2.65 17.2 4.29 -17.2
muculus_musculus_discors 1 0 % 0 % -34.1 7.84 -4.84 -7.48 4.72 -5.51 -18.2 -25 28.6 -0.0706 30.4 0.38 11 4.11 0.614
mytilus_sp 0.33 0 % 13.6 % -66.2 -0.475 -1.63 6.15 -2.19 -1.93 -3.5 6.32 -6.01 0.0241 1.47 -0.54 0.279 -650 0.54
nematoda 0.33 27.3 % 18.2 % -0.274 -0.633 1.63 -1.63 0.087 -2.34 2.52 -1.75 2.94 1.03 -3.19 -0.0969 -0.686 0.539 -0.00813
nemertea 1 0 % 13.6 % -65.2 100 78.4 -38.3 64.1 46.3 32.8 52.8 -58.4 -125 -135 12.2 -1.4 1.18 2.72
neoleanira_tetragona 1 0 % 27.3 % -117 71.3 317 338 93.9 215 -96 346 -390 -169 -675 -20.6 22.8 6.5 2.64
nephtyidae_spp -7.28 0 % 18.2 % -3.17e+15 -2.8e+14 -6.51e+14 2.14e+14 -6.34e+14 -1.31e+14 -1.93e+15 1.47e+15 -9.11e+14 -1.09e+15 2.47e+15 7.48e+13 9.42e+14 -1.54e+14 2.45e+14
nephtys_caeca 0.39 0 % 4.5 % -42.4 2.89 0.211 5.94 -5.06 1.54 -0.631 2.12 -9.67 -5.76 0.695 0.639 -0.173 -385 -6.63
nephtys_incisa 0.31 13.6 % 36.4 % -72.8 -27.1 6.45 2.59 1.25 10.7 -0.395 7.84 -15 19.8 -8.93 0.11 0.0158 -714 -0.663
nephtys_sp 1 0 % 13.6 % -179 -350 -103 -9.43 189 -62.4 -52.4 38.3 131 443 -234 1.7 -90.3 1.7 -175
nuculana_minuta 0.83 4.5 % 27.3 % -218 -326 89.4 -121 50.6 -22 5 193 -212 493 -197 -24.7 -3.03 0.443 15.2
nymphonidae_spp 1 0 % 9.1 % -116 72.2 -19.5 58.3 -72 96.9 -21.5 181 -373 -162 106 19.7 1.69 0.641 -71.6
oenopota_sp 0.29 4.5 % 9.1 % -503 6.23 -7.07 1.53 3.35 -2.22 -2.66 1.39 0.386 -4.57 6.13 0.276 -1674 -569 1.78
oligochaeta 0.66 4.5 % 22.7 % -66.1 -17.8 26 23.6 -6.43 -11 26.8 -58.8 62.5 19.7 -68.5 0.349 -21 2.11 -149
ophelia_limacina 1 0 % 31.8 % -262 -229 87.4 -88.3 149 26.1 83.5 15.1 6.65 267 -407 -90.1 -128 1.41 -363
opheliidae_spp 1 0 % 9.1 % -364 -797 -905 -430 184 -842 -133 -1142 1799 1328 1031 -252 25.1 78.3 -154
ophiopholis_aculeata -2.79 0 % 13.6 % -1.76e+15 -9.67e+14 1.08e+15 3.3e+15 4.12e+14 1.64e+15 -1.36e+15 2.55e+15 -3.23e+15 -1.4e+14 -4.04e+15 -3.57e+14 2.46e+14 -2.66e+14 -8.17e+14
ophiura_robusta 1 0 % 22.7 % -363 1057 384 510 -238 328 -114 992 -1732 -1436 -247 22.7 14.7 3.72 -260
orchomenella_minuta 1 0 % 22.7 % -44.6 -36.8 88.6 118 15.8 71.7 -28.3 145 -162 -16.3 -213 1.59 -0.402 -3.6 -3.16
ostracoda 0.24 18.2 % 40.9 % -52.1 2.01 4.55 2.39 1.05 1.22 1.48 1.04 -2.1 -2.17 -8.56 -1.27 -0.0592 -525 1.34
pagurus_sp 1 0 % 4.5 % -116 -59.1 -150 -27.3 -12.7 -21.3 -16.8 -0.26 32.3 90.1 168 -139 -103 4.06 43.7
pagurus_pubescens 1 0 % 4.5 % -201 266 149 12.2 -1.55 365 125 359 -829 -500 -84.8 -25.2 -67 3.56 27.9
pandalus_montagui 1 0 % 13.6 % -98.1 43.3 -238 277 -87.6 -105 -13.6 53.1 -28.8 -82.1 106 2.11 -25.9 5.99 2.43
parathyasira_equalis 1 0 % 4.5 % -137 231 -386 -281 81.1 -24.7 6.45 -79.1 129 -112 592 -11.4 -12.5 16.4 155
parvicardium_pinnulatum 1 0 % 31.8 % -1836 -1999 -984 -2306 115 1031 -232 1415 -2848 3730 1278 25.7 -23.2 37.5 -288
periploma_leanum 1 0 % 18.2 % -224 -497 370 566 277 298 -203 527 -403 339 -1291 22.7 -16.5 6.89 -20.1
philine_lima 1 0 % 4.5 % -116 -59.1 -150 -27.3 -12.7 -21.3 -16.8 -0.26 32.3 90.1 168 -139 -103 4.06 43.7
philomedes_sp 1 0 % 13.6 % -213 -176 -190 -107 228 -421 137 -512 858 530 -131 -61.2 -37.1 39 48.9
pholoe_longa 1 0 % 13.6 % -105 -379 -49.5 30.9 89.5 -32.5 -104 44.4 139 409 -150 -5.97 -0.224 1.01 -14.7
pholoe_sp 0.24 45.5 % 36.4 % -56.5 3.77 2.63 4.87 -0.204 2 1.21 3.46 -6.34 -5.59 -6.74 0.0688 -1.61 -584 0.953
phoxocephalus_holbolli 0.5 4.5 % 22.7 % 65.8 10.7 6.83 11.7 -7.81 1.52 1.3 12.6 -21.8 -17.2 -8.85 0.788 -7.62 741 -2.15
polynoidae_spp 0.19 4.5 % 54.5 % -72.2 -1.8 4.12 1.44 0.0749 2.79 0.521 3.83 -4.86 -0.0527 -7.18 -2.58 -0.983 -732 0.0986
pontogeneia_inermis 1 0 % 4.5 % -129 -215 -104 -102 38.7 -185 -18.5 -237 405 346 120 -167 7.09 17.4 3.1
pontoporeia_femorata 0.41 18.2 % 36.4 % -222 -1.86 -9.72 2.61 -5.68 1.72 2.69 0.785 -1.09 0.677 9.32 0.309 -541 -715 -16.7
praxillella_praetermissa 0.46 0 % 18.2 % -65.8 -15.6 -9.82 -1.76 1.35 5.46 3.83 0.238 -4.52 12.3 8.79 0.165 -38.2 -526 3.59
propebela_turricula 1 0 % 13.6 % -638 424 316 1228 -364 -1066 28.4 1038 -728 -621 -649 18.5 -1.02 -15.1 146
protomedeia_fasciata 0.57 4.5 % 22.7 % -13.5 -9.76 -16.4 36.7 -14.8 -25.2 -6.85 -22.2 28.7 6.41 8.38 -0.515 2.51 1.71 -4.04
protomedeia_grandimana 0.21 18.2 % 59.1 % -62.9 -2.75 1.93 4.73 0.15 2.14 -0.584 3.75 -3.66 1.49 -6.93 -0.285 -0.233 -652 0.407
puncturella_noachina 1 4.5 % 4.5 % -65.2 100 78.4 -38.3 64.1 46.3 32.8 52.8 -58.4 -125 -135 12.2 -1.4 1.18 2.72
quasimelita_formosa 0.23 4.5 % 27.3 % -1.98 -4.19 -2.85 -3.92 2.67 -1.49 0.365 -0.892 3.72 8.18 0.936 -0.396 -0.169 0.728 0.528
quasimelita_quadrispinosa 1 0 % 13.6 % -98.3 -340 162 83.2 -61.1 154 9.94 37.7 -163 246 -197 -4.03 10.6 3.64 -29.9
retusa_obtusa -3.46 0 % 22.7 % -3.22e+15 -2.68e+15 2.84e+15 4.04e+15 -2.14e+15 -2.69e+15 -1.03e+15 -2.53e+15 3.67e+15 2.32e+15 -2.51e+15 -1.66e+14 6.42e+14 8.13e+13 -5.4e+14
sabellidae_spp 0.3 0 % 4.5 % -4.01 0.376 4.07 2.69 3.29 3.82 -2.65 7.25 -7.07 -4.26 -8.97 1.36 -1.47 -0.577 -2.95
scoletoma_fragilis 0.45 4.5 % 22.7 % -28.5 -33.3 29 12.1 -2.76 17.9 -9.3 19.1 -14.7 22 -36.6 -6.12 0.38 -0.472 -40
scoletoma_sp 1 0 % 4.5 % -56.2 89.2 11.5 -96.9 52.1 7.91 8.08 -18.9 20.2 -74.7 39.6 14.5 9.06 4.54 -2.85
scoloplos_sp 0 0 % 4.5 % -26.6 -2.33e-14 -3.96e-14 -6.51e-14 3.04e-15 -1.61e-14 -1.36e-14 -2.49e-14 4.32e-14 4.04e-14 1.1e-13 1.1e-15 1.9e-15 7.81e-16 1.32e-15
serripes_groenlandicus 1 0 % 9.1 % -480 215 50.5 -428 68.4 304 -248 -441 269 -150 809 -312 148 106 184
sipuncula 0.18 0 % 18.2 % -63.9 -4.9 1.17 2.69 1.93 2.51 -1.22 3.81 -3.92 3.5 -5.3 0.187 -1.01 -637 -0.191
solamen_glandula 0 0 % 4.5 % -26.6 -2.33e-14 -3.96e-14 -6.51e-14 3.04e-15 -1.61e-14 -1.36e-14 -2.49e-14 4.32e-14 4.04e-14 1.1e-13 1.1e-15 1.9e-15 7.81e-16 1.32e-15
solariella_sp 0.53 0 % 9.1 % -121 -210 19.4 -19.6 -17.8 11.1 3.45 32 -72.2 208 9.7 -0.541 2.03 -620 -2.4
strongylocentrotus_sp 1 4.5 % 0 % -46.7 -22.5 -13.5 -4.54 -9.71 -39.7 8.79 -90.9 111 38.5 22.2 -19 10.6 7.25 -2.62
tachyrhynchus_erosus 0 0 % 4.5 % -26.6 -2.33e-14 -3.96e-14 -6.51e-14 3.04e-15 -1.61e-14 -1.36e-14 -2.49e-14 4.32e-14 4.04e-14 1.1e-13 1.1e-15 1.9e-15 7.81e-16 1.32e-15
thracia_septentrionalis 0.18 4.5 % 9.1 % -61.2 6.36 -0.526 -1.02 1.46 0.396 0.443 1.24 -2.44 -6.27 0.429 0.521 -0.0902 -616 -0.868
thyasira_gouldi 0.32 22.7 % 45.5 % -86 -15.9 8.45 0.487 1.46 10.4 0.717 8.99 -15 10.2 -11.1 0.246 -0.172 -865 1.29
thyasira_sp 0 0 % 4.5 % -26.6 -2.33e-14 -3.96e-14 -6.51e-14 3.04e-15 -1.61e-14 -1.36e-14 -2.49e-14 4.32e-14 4.04e-14 1.1e-13 1.1e-15 1.9e-15 7.81e-16 1.32e-15
trichotropis_bicarinata 1 0 % 4.5 % -87.7 -19.3 -28.5 -85.4 95.6 -71.5 -1.94 -25.7 120 126 -3.27 -36.2 4 5.12 16.8
turritellopsis_stimpsoni -7.31 0 % 18.2 % -1.83e+15 3.77e+15 1.02e+15 3.6e+15 7.89e+13 1.13e+15 1.36e+15 8.37e+14 -3.13e+15 -4.53e+15 -4.62e+15 -6.14e+14 -1.13e+14 -1.26e+14 2.14e+14
yoldia_myalis 1 0 % 9.1 % -461 61.9 -883 -121 254 619 125 443 -1055 -335 843 -26 -197 23.6 -1.01

Prediction of specific richness based on this model:

Density data

Here, we considered density data with a Poisson distribution.

Abiotic parameters

Influence indices

2.2. Hierarchical Modelling of Species Communities

First, we initiate the HMSC model with the chosen data, priors and parameters.

HMSC_model <- hmsc(HMSC_data, HMSC_param, HMSC_prior, family = "overPoisson", niter = 100000, nburn = 1000, thin = 100)

Here are the diagnostics to evaluate each model’s quality.

Human activities

Trace plots

Explanatory power

Confidence intervals

Variance partitioning

Habitat parameters

Trace plots

Explanatory power

Confidence intervals

Variance partitioning

All variables

Trace plots

Explanatory power

Confidence intervals

Variance partitioning

Finally, we can predict the values of our parameters within BSI.

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